Biblio

Found 29 results
Filters: Keyword is Proteins  [Clear All Filters]
2016
Marchand J.-R., Lolli G., Caflisch A..  2016.  Derivatives of 3-amino-2-methylpyridine as BAZ2B bromodomain ligands: In silico discovery and in crystallo validation. Journal of Medicinal Chemistry. 59(21):9919-9927.
Unzue A., Zhao H., Lolli G., Dong J., Zhu J., Zechner M., Dolbois A., Caflisch A., Nevado C..  2016.  The "gatekeeper" residue influences the mode of binding of acetyl indoles to bromodomains. Journal of Medicinal Chemistry. 59(7):3087-3097.
Lolli G., Caflisch A..  2016.  High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-Ray crystallography. ACS Chemical Biology. 11(3):800-807.
2014
Fu B., Sahakyan A.B, Camilloni C., Tartaglia G.G, Paci E., Caflisch A., Vendruscolo M., Cavalli A..  2014.  ALMOST: An all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry. 35(14):1101-1105.
2013
Kalgin I.V, Caflisch A., Chekmarev S.F, Karplus M..  2013.  New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: Application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry B. 117(20):6092-6105.
2011
Scalco R., Caflisch A..  2011.  Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B. 115(19):6358-6365.
Zhao H., Huang D..  2011.  Hydrogen bonding penalty upon ligand binding. PLoS One. 6(6):e19923.
Seeber M., Felline A., Raimondi F., Muff S., Friedman R., Rao F., Caflisch A., Fanelli F..  2011.  Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32(6):1183-1194.
2009
Brooks B.R, Brooks III C.L, Mackerell A.D, Nilsson L., Petrella R.J, Roux B., Won Y., Archontis G., Bartels C., Boresch S. et al..  2009.  CHARMM: The biomolecular simulation program. Journal of Computational Chemistry. 30(10):1545-1614.
Muff S., Caflisch A..  2009.  Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics. 130(12):125104.
Benedix A., Becker C.M, de Groot B.L, Caflisch A., Böckmann R.A.  2009.  Predicting free energy changes using structural ensembles. Nat Methods. 6(1):3-4.
2008
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
Krivov S.V, Muff S., Caflisch A., Karplus M..  2008.  One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process. The Journal of Physical Chemistry B. 112(29):8701-8714.
2007
Seeber M., Cecchini M., Rao F., Settanni G., Caflisch A..  2007.  Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics. 23(19):2625-2627.
2006
Kolb P., Caflisch A..  2006.  Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49(25):7384-7392.
Caflisch A..  2006.  Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10(5):437-444.
2005
Rao F., Settanni G., Guarnera E., Caflisch A..  2005.  Estimation of protein folding probability from equilibrium simulations. Journal of Chemical Physics. 122(18):184901.
Tartaglia G.G, Pellarin R., Cavalli A., Caflisch A..  2005.  Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science. 14(10):2735-2740.
Böckmann R.A, Caflisch A..  2005.  Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88(5):3191-3204.
2004
Caflisch A..  2004.  Protein folding: Simple models for a complex process. Structure. 12(10):1750-1752.
Tartaglia G.G, Cavalli A., Pellarin R., Caflisch A..  2004.  The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Science. 13(7):1939-1941.
2003
Uk B., Taufer M., Stricker T., Settanni G., Cavalli A., Caflisch A..  2003.  Combining task- and data parallelism to speed up protein folding on a desktop grid platform. Proceedings of the 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2003).
Haberthür U., Majeux N., Werner P., Caflisch A..  2003.  Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. Journal of Computational Chemistry. 24(15):1936-1949.
Cavalli A., Haberthür U., Paci E., Caflisch A..  2003.  Fast protein folding on downhill energy landscape. Protein Science. 12(8):1801-1803.
Caflisch A..  2003.  Folding for binding or binding for folding? Trends in Biotechnology. 21(10):423-425.

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